It's all in the manual, why don't people read it.
From your manual page ix
3 x PCIe 3.0 x1 slots *
The PCIe x16_3 slot shares bandwidth with SATA6G_5 and SATA6G_6 <== an M.2 socket is NOT a PCIe slot <= so no, it they won't be disabled.
From your manual page x
When the M.2_1 Socket 3 is operating in SATA mode, SATA6G_2 port will be disabled <== Doesn't apply either. Sata PORT 2 will only get disabled if M.2_1 is being used by a SATA device. Going by your post, it's not occupied at all. So sata2 will remain operational. If you install an M.2 device in M.2_1 sata 2 will ONLY get disabled IF you insert a sata based M.2 device. If you were to add another PCIe device like that 970 evo, sata 2 will remain operational